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Yorodumi- PDB-3gaf: 2.2A Crystal Structure of 7-Alpha-Hydroxysteroid Dehydrogenase fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3gaf | ||||||
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Title | 2.2A Crystal Structure of 7-Alpha-Hydroxysteroid Dehydrogenase from Brucella Melitensis | ||||||
Components | 7-ALPHA-HYDROXYSTEROID DEHYDROGENASE | ||||||
Keywords | OXIDOREDUCTASE / BRUCELLA / MELITENSIS / HYDROXYSTEROID / DEHYDROGENASE / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / SSGCID / STRUCTURAL GENOMICS | ||||||
Function / homology | Function and homology information 7alpha-hydroxysteroid dehydrogenase / cholate 7-alpha-dehydrogenase activity Similarity search - Function | ||||||
Biological species | Brucella melitensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å | ||||||
Authors | Seattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
Citation | Journal: To be Published Title: 2.2A Crystal Structure of 7-Alpha-Hydroxysteroid Dehydrogenase from Brucella Melitensis Authors: Seattle Structural Genomics Center for Infectious Disease | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3gaf.cif.gz | 347.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gaf.ent.gz | 283.8 KB | Display | PDB format |
PDBx/mmJSON format | 3gaf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ga/3gaf ftp://data.pdbj.org/pub/pdb/validation_reports/ga/3gaf | HTTPS FTP |
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-Related structure data
Related structure data | 1ahiS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 26339.078 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Brucella melitensis (bacteria) / Strain: BIOVAR ABORTUS 2308 / Gene: BMEI0406 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q8YIN7, 7alpha-hydroxysteroid dehydrogenase #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.54 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion / pH: 4 Details: 20% PEG 1500, 0.1M MIB buffer/salt, pH 4.0, VAPOR DIFFUSION, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å | ||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: SATURN 944 / Detector: CCD / Date: Jan 1, 2008 / Details: MULTI-LAYER OPTICS MIRRORS | ||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.2→50 Å / Num. obs: 99242 / % possible obs: 99.1 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 25.188 | ||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Rfactor: 34.97 / Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1AHI Resolution: 2.2→48.51 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.932 / Occupancy max: 1 / Occupancy min: 1 / SU B: 6.517 / SU ML: 0.164 / Cross valid method: THROUGHOUT / ESU R: 0.27 / ESU R Free: 0.212 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.168 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→48.51 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.201→2.258 Å / Total num. of bins used: 20
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